6W4Y

Structure of full-length human lambda-6A light chain JTO in complex with hydantoin stabilizer

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MG4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	20% PEG 3350 and 0.25 M NH4H2PO4 at 23 degrees C

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.713	α = 90
b = 82.341	β = 90
c = 95.912	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2019-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976484	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.91	44.65	99.9	0.066	0.025	1	22.7	8		39919

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	2.01	99.4		0.066	0.025	0.92		8.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6MG4	1.91	44.65	37905	1952	99.85	0.1832	0.1807	0.2322	RANDOM	33.161

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.95			3.79		-1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.122
r_dihedral_angle_4_deg	15.037
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_1_deg	7.449
r_angle_refined_deg	1.586
r_angle_other_deg	1.367
r_chiral_restr	0.069
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.122
r_dihedral_angle_4_deg	15.037
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_1_deg	7.449
r_angle_refined_deg	1.586
r_angle_other_deg	1.367
r_chiral_restr	0.069
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3260
Nucleic Acid Atoms
Solvent Atoms	401
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.